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J Integr Bioinform. 2015 Sep 4;12(2):269. doi: 10.2390/biecoll-jib-2015-269.

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

Abstract

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

PMID:
26528567
DOI:
10.2390/biecoll-jib-2015-269
[Indexed for MEDLINE]

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